Nothing
mapCODs<-function(D){
COD=D$COD #start with vec of integers. Map to a vec of Strings
# CODS=rep("other",length(COD))
CODS=rep("other",dim(D)[1]) #set default to "other" type of death
# get mappings from https://seer.cancer.gov/codrecode/1969+_d09172004/index.txt
CODS[COD==41000]=NA
CODS[COD==0]="alive"
# Use same names as in cancer incidence as much as possible
CODS[(COD>=20010)&(COD<=20100)]="oral"
CODS[COD==21010]="esophagus"
CODS[COD==21020]="stomach"
CODS[COD==21030]="intestine"
CODS[COD==21040]="colon"
CODS[COD%in%c(21050,21060)]="rectal"
CODS[COD%in%c(21071,21072)]="liver"
CODS[COD%in%c(21080,21090)]="gallBladder"
CODS[COD==21100]="pancreas"
CODS[COD%in%c(21110,21120)]="peritonium"
CODS[COD==21130]="GI"
CODS[COD%in%c(21110,21120)]="peritonium"
CODS[COD==22010]="sinus"
CODS[COD==22020]="larynx"
CODS[COD==22030]="lung"
CODS[COD==22050]="pleura"
CODS[COD%in%c(22060,32020)]="thymus"
CODS[COD==23000]="bone"
CODS[COD==24000]="HnN"
CODS[COD==25010]="melanoma"
CODS[COD==25020]="skin"
CODS[COD==26000]="breast"
CODS[COD==27010]="cervix"
CODS[COD%in%c(27020,27030)]="uterus"
CODS[COD==27040]="ovary"
CODS[COD%in%c(27050,27060,27070)]="femGen"
CODS[COD==28010]="prostate"
CODS[COD==28020]="testes"
CODS[COD%in%c(28030,28040)]="maleGen"
CODS[COD==29010]="bladder"
CODS[COD%in%c(29020,29030,29040)]="renal"
CODS[COD==30000]="eye"
CODS[COD==31010]="brain"
CODS[COD==32010]="thyroid"
CODS[COD==32010]="HL"
CODS[COD==33040]="NHL"
CODS[COD==34000]="MM"
CODS[COD==35011]="ALL"
CODS[COD==35012]="CLL"
CODS[COD%in%c(35021,35031)]="AML"
CODS[COD==35022]="CML"
CODS[COD%in%c(35013,35023,35041,35043)]="OL"
CODS[COD%in%c(36010,36020,37000)]="otherMalig" #Mesothelioma ;Kaposi Sarcoma ;Miscellaneous Malignant Cancer;
CODS[COD==38000]="benign"
### these didn't map
# AMLti, APL breastCIS, cervixCIS CMML femGenCIS, giCIS, guCIS, HCL, LGL,
# maleGenCIS, MDS, MPN, nerves, other, otherCIS respCIS, skinCIS, SLL, unknown
CODS[COD%in%c(50000,50010,50030,50040)]="infection"
CODS[COD==50050]="diabetes"
CODS[COD==50051]="alzheimers"
CODS[COD==50060]="heart"
CODS[COD==50070]="hypertension"
CODS[COD==50080]="cerebroVasc"
CODS[COD==50090]="athero"
CODS[COD==50100]="aneurysm"
CODS[COD==50110]="otherVasc"
CODS[COD==50120]="pneumonia"
CODS[COD==50130]="COPD"
CODS[COD==50140]="ulcer"
CODS[COD==50150]="livFail"
CODS[COD==50160]="renFail"
CODS[COD%in%c(50170,50190)]="birthing"
CODS[COD==50180]="congenDef"
CODS[COD%in%c(50200,50300)]="other" #Symptoms, Signs and Ill-Defined Conditions +Other
CODS[COD==50210]="accidents"
CODS[COD==50220]="suicide"
CODS[COD==50230]="homocide"
# CODS=as.factor(CODS)
# CODS
D$CODS=as.factor(CODS)
D
}
# > table(d$COD,useNA="always")
# 0 20010 20020 20030 20040 20050 20060 20070 20080 20090 20100 21010 21020 21030 21040
# 4291579 479 15586 4913 1695 9289 5500 4695 4609 3322 10469 84044 99606 8183 314870
# 21050 21060 21071 21072 21080 21090 21100 21110 21120 21130 22010 22020 22030 22050 22060
# 61830 4338 84712 22767 14739 11921 217308 1983 4276 5987 3251 25226 959251 2617 2076
# 23000 24000 25010 25020 26000 27010 27020 27030 27040 27050 27060 27070 28010 28020 28030
# 8543 26078 51929 12574 263225 26121 22419 26360 92240 2820 5268 2599 172641 2762 1374
# 28040 29010 29020 29030 29040 30000 31010 32010 32020 33010 33040 34000 35011 35012 35013
# 315 94125 76870 2717 2522 1812 86342 9366 5837 9416 133827 66092 10523 23907 3015
# 35021 35022 35023 35031 35041 35043 37000 38000 41000 50000 50010 50030 50040 50050 50051
# 55564 10102 4613 1246 15650 17320 259226 50141 83211 843 35 31119 47310 52261 50230
# 50060 50070 50080 50090 50100 50110 50120 50130 50140 50150 50160 50170 50180 50190 50200
# 629721 21364 133618 14507 12032 8797 72133 134635 5729 22419 37569 342 2458 125 21923
# 50210 50220 50230 50300 <NA>
# 46647 14579 1705 279381 0
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